Quantitative analysis of the antifungal drug anidulafungin by LC-online SPE-MS/MS in human plasma

The objective of this study was to develop a fast and robust method for the quantitation of the antifungal drug anidulafungin in human plasma samples by generic two-dimensional liquid chromatography (online-SPE/reversed phase LC) coupled to a tandem-quadrupole mass spectrometer (LC-online SPE-MS/MS). Online SPE was performed using an Oasis HLB cartridge column and for reversed-phase chromatography a Nucleodur Gravity C(18) column was used. A 100 μL aliquot of human plasma was extracted with 200 μL of 80:20 MeOH-0.2 M ZnSO(4) (v/v) as precipitation reagent containing ascomycin as internal standard (IS). The supernatant was directly injected for analysis. The total run time was 4.5 min. Anidulafungin and ascomycin were detected in the positive ionization mode. The method performance data for anidulafungin, such as limit of detection (0.013 μg/mL), lower limit of quantitation (0.04 μg/mL), linearity (R(2) = 0.9999) and concentration range (0.04-10 μg/mL) were ascertained. Intra- and inter-day precisions were ≤6.6% and intra- and inter-day accuracies were 98.5-101.0 and 100.0-102.5%, respectively. The assay was successfully applied for quantitation of anidulafungin in patient plasma samples.     

Evaluation of small mass spectrometer systems for permanent gas analysis

This work is aimed at understanding the aspects of designing a miniature mass spectrometer (MS) system. Several types of small MS systems are evaluated and discussed, including linear quadrupole, quadrupole ion trap, time of flight, and sector. Analysis of hydrogen, helium, oxygen, and argon in a nitrogen background with the concentrations of the components of interest ranging from 0 to 5000 parts per million (ppm). The performance of each system in terms of accuracy, precision, limits of detection, response time, recovery time, scan rate, size, and weight is assessed. The relative accuracies of the systems varied from <1% to approximately 40% with an average below 10%. Relative precisions varied from 1% to 20%, with an average below 5%. The detection limits had a large distribution, ranging from 0.2 to 170 ppm. The systems had a diverse response time ranging from 4 to 210 s, as did the recovery time with a 6-to-210-s distribution. Most instruments had scan times near 1 s; however, one instrument exceeded 13 s. System weights varied from 9 to 52 kg and sizes ranged from 15 x 10(3) cm3 to 110 x 10(3) cm3. A performance scale is set up to rank each system, and an overall performance score is given to each system.     

Real-time quantitative analysis of H2, He,O2, and Ar by quadrupole ion trap mass spectrometry

The use of a quadrupole ion trap mass spectrometer (QITMS) for quantitative analysis of hydrogen and helium as well as of other permanent gases is demonstrated. Like commercial instruments, the customized QITMS uses mass selective instability; however, this instrument operates at a greater trapping frequency and without a buffer gas. Thus, a useable mass range from 2 to over 50 daltons (Da) is achieved. The performance of the ion trap is evaluated using part-per-million (ppm) concentrations of hydrogen, helium, oxygen, and argon mixed into a nitrogen gas stream, as outlined by the National Aeronautics and Space Administration (NASA), which is interested in monitoring for cryogenic fuel leaks within the Space Shuttle during launch preparations. When quantitating the four analytes, relative accuracy and precision were better than the NASA-required minimum of 10% error and 5% deviation, respectively. Limits of detection were below the NASA requirement of 25-ppm hydrogen and 100-ppm helium; those for oxygen and argon were within the same order of magnitude as the requirements. These results were achieved at a fast data recording rate, and demonstrate the utility of the QITMS as a real-time quantitative monitoring device for permanent gas analysis.     

What induces pocket openings on protein surface patches involved in protein–protein interactions?

We previously showed for the proteins BCL-X_L, IL-2, and MDM2 that transient pockets at their protein–protein binding interfaces can be identified by applying the PASS algorithm to molecular dynamics (MD) snapshots. We now investigated which aspects of the natural conformational dynamics of proteins induce the formation of such pockets. The pocket detection protocol was applied to three different conformational ensembles for the same proteins that were extracted from MD simulations of the inhibitor bound crystal conformation in water and the free crystal/NMR structure in water and in methanol. Additional MD simulations studied the impact of backbone mobility. The more efficient CONCOORD or normal mode analysis (NMA) techniques gave significantly smaller pockets than MD simulations, whereas tCONCOORD generated pockets comparable to those observed in MD simulations for two of the three systems. Our findings emphasize the influence of solvent polarity and backbone rearrangements on the formation of pockets on protein surfaces and should be helpful in future generation of transient pockets as putative ligand binding sites at protein–protein interfaces. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phospholipid bilayer free volume analysis employing the thermal ring-closing reaction of merocyanine molecular switches

The free volume properties of phospholipid bilayers have been determined using a new assay that applies the photochromic and solvatochromic properties of merocyanines. The orientation and embedding depth of the merocyanines in the bilayer are controlled using substitution on the merocyanine indole moiety. The free volume changes at the aqueous interface (region 1), the phospholipid headgroup (region 2), and the aliphatic interior (region 3) of the bilayer are compared by analyzing the rate constants for the merocyanine ring-closing reaction. Free volume variations during the P(beta)(')(gel) <--> L(alpha)(liquid) phase transition are observed in region 1, in accordance with large structural rearrangements between the gel and the liquid phases in this region. The largest free volume is found in region 3, and the smallest is found in region 2. This distribution of free volume in the bilayer agrees with computational studies of these systems. Comparison of the free volume in region 2 of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids shows that this method is sensitive to small structural differences between lipids. In region 2, the free volume is found to be approximately 2 times larger in DPPC bilayers, which could be related to different merocyanine interactions with the two phosphatidylcholines. Free volume properties determined on picosecond and second time scales are compared based on an analysis of merocyanine formation and decoloration reactions.     

Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.